[gmx-users] template.cpp compilation problem with Gromacs 5.0.4
Dear Gromacs users I would like to code my own analysis programs but I'm facing problems with template.cpp compilations with gromacs 5.0.4. Made source GMXRC. cmake goes nicely but make does not make it. Any suggestions? downgrade? Here goes cmake and make output. Thanks a lot Milton $mkdir build $cd build $ cmake .. -- The C compiler identification is GNU 4.8.2 -- The CXX compiler identification is GNU 4.8.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PkgConfig: /usr/bin/pkg-config (found version 0.26) -- checking for module 'libgromacs' -- found libgromacs, version 5.0.4 -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Boost version: 1.55.0 -- Found GROMACS: /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so GROMACS version 5.0.0 found -- Configuring done -- Generating done -- Build files have been written to: /home/milton/pesq/bta/progs/template/build $make Scanning dependencies of target template [100%] Building CXX object CMakeFiles/template.dir/template.cpp.o In file included from /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:49:0, from /usr/local/gromacs/include/gromacs/analysisdata.h:209, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:81:12: error: ‘std::move’ has not been declared using std::move; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:85:13: error: ‘unique_ptr’ in namespace ‘std’ does not name a type typedef std::unique_ptrT type; ^ In file included from /usr/local/gromacs/include/gromacs/analysisdata.h:209:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:249:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractAverageHistogram’ does not name a type typedef gmx_unique_ptrAbstractAverageHistogram::type ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:283:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer resampleDoubleBinWidth(bool bIntegerBins) const; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:295:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer clone() const; ^ In file included from /usr/local/gromacs/include/gromacs/options/basicoptions.h:54:0, from /usr/local/gromacs/include/gromacs/options.h:149, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/abstractoption.h:73:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractOptionStorage’ does not name a type typedef gmx_unique_ptrAbstractOptionStorage::type ^ /usr/local/gromacs/include/gromacs/options/abstractoption.h:123:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const = 0; ^ In file included from /usr/local/gromacs/include/gromacs/options.h:149:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/basicoptions.h:101:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const;
[gmx-users] template.cpp compilation problem with Gromacs 5.0.4
Dear Gromacs users I would like to code my own analysis programs but I'm facing problems with template.cpp compilations with gromacs 5.0.4. Made source GMXRC. cmake goes nicely but make does not make it. Any suggestions? downgrade? Here goes cmake and make output. Thanks a lot Milton $mkdir build $cd build $ cmake .. -- The C compiler identification is GNU 4.8.2 -- The CXX compiler identification is GNU 4.8.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PkgConfig: /usr/bin/pkg-config (found version 0.26) -- checking for module 'libgromacs' -- found libgromacs, version 5.0.4 -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for GromacsVersion in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_mtop in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for output_env_done in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for gmx_nonbonded_setup in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found -- Boost version: 1.55.0 -- Found GROMACS: /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so GROMACS version 5.0.0 found -- Configuring done -- Generating done -- Build files have been written to: /home/milton/pesq/bta/progs/template/build $make Scanning dependencies of target template [100%] Building CXX object CMakeFiles/template.dir/template.cpp.o In file included from /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:49:0, from /usr/local/gromacs/include/gromacs/analysisdata.h:209, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:81:12: error: ‘std::move’ has not been declared using std::move; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:85:13: error: ‘unique_ptr’ in namespace ‘std’ does not name a type typedef std::unique_ptrT type; ^ In file included from /usr/local/gromacs/include/gromacs/analysisdata.h:209:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:249:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractAverageHistogram’ does not name a type typedef gmx_unique_ptrAbstractAverageHistogram::type ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:283:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer resampleDoubleBinWidth(bool bIntegerBins) const; ^ /usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:295:9: error: ‘AverageHistogramPointer’ does not name a type AverageHistogramPointer clone() const; ^ In file included from /usr/local/gromacs/include/gromacs/options/basicoptions.h:54:0, from /usr/local/gromacs/include/gromacs/options.h:149, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/abstractoption.h:73:9: error: ‘type’ in ‘struct gmx::gmx_unique_ptrgmx::AbstractOptionStorage’ does not name a type typedef gmx_unique_ptrAbstractOptionStorage::type ^ /usr/local/gromacs/include/gromacs/options/abstractoption.h:123:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const = 0; ^ In file included from /usr/local/gromacs/include/gromacs/options.h:149:0, from /usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280, from /home/milton/pesq/bta/progs/template/template.cpp:38: /usr/local/gromacs/include/gromacs/options/basicoptions.h:101:17: error: ‘AbstractOptionStoragePointer’ does not name a type virtual AbstractOptionStoragePointer createStorage() const;
